Detecting SARS-CoV-2 Variants Earlier in Wastewater

Scripps Research
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A team from Scripps Research and the University of California, San Diego, in collaboration with the San Diego Epidemiology and Research for COVID Health (SEARCH) alliance, reports that with just two teaspoons of raw sewage, they can accurately determine the genetic mixture of SARS-CoV-2 variants present within a population and identify new variants of concern up to 14 days before traditional clinical testing.

In San Diego wastewater, the group detected the Omicron variant 11 days before it was first reported clinically.

Their algorithm, named “Freyja”, for identifying SARS-CoV-2 variants in wastewater, described in an article “Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission” in Nature, has been adapted by many public health labs, and is a boon to surveillance efforts that aim to detect new variants of SARS-CoV-2, say the scientists.

“As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases,” write the investigators.

“SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples.

Improved protocols for detecting COVID variants in wastewater

“Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples and identify multiple instances of virus spread not captured by clinical genomic surveillance.

“Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.”

“In a lot of places, standard clinical surveillance for new variants of concern is not only slow but extremely cost-prohibitive,” explains Kristian Andersen, PhD, professor of Immunology and Microbiology at Scripps Research and a senior author of the new work. “But with this new tool, you can take one wastewater sample and basically profile the whole city.”

The project required a tight collaboration between hospitals, state, and local governments, sequencing facilities, and academic scientists–including researchers in the Andersen lab and that of UC San Diego microbiologist Rob Knight, PhD.

“It took a lot of collaboration between public health and academic players to get this system established in San Diego, and now that we’ve shown its effectiveness, we hope it inspires other localities to use these tools,” says Knight. “We’re also excited about expanding them to pathogens beyond SARS-CoV-2.”

The researchers note that they are continuing to improve upon the set of tools they use to analyze viruses in wastewater, but that the current suite of methods is already a leap forward from previous approaches.

Additional articles on sampling wastewater for COVID-19 analysis can be found in GEN: “New Methods Enable Earlier Detection of COVID-19 Outbreaks in Wastewater,” Water Research: “Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater,” and Science of the Total Environment: “Five-week warning of COVID-19 peaks prior to the Omicron surge in Detroit, Michigan using wastewater surveillance.”

Wastewater samples for covid-19 analysis.

Wastewater samples for covid-19 analysis.